<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:14pt"><br><div style="font-family: times new roman, new york, times, serif; font-size: 14pt;"><div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"><div id="yiv69668406"><div style="color:#000;background-color:#fff;font-family:times new roman, new york, times, serif;font-size:14pt;"><div style="font-family:times new roman, new york, times, serif;font-size:14pt;"><div style="font-family:times new roman, new york, times, serif;font-size:12pt;"><div id="yiv69668406"><div style="color:#000;background-color:#fff;font-family:times new roman, new york, times, serif;font-size:14pt;"><div>Deer users</div><div><br></div><div><span id="yiv69668406result_box" class="yiv69668406" lang="en"><span class="yiv69668406hps">The simulation</span> <span class="yiv69668406hps">box contains</span> <span
 class="yiv69668406hps">sodium</span> <span class="yiv69668406hps">and chloride</span> <span class="yiv69668406hps">ions</span></span></div><div><span id="yiv69668406result_box" class="yiv69668406" lang="en"><span class="yiv69668406hps"><br></span></span></div><div><span id="yiv69668406result_box" class="yiv69668406" lang="en"><span class="yiv69668406hps">start simulation</span></span></div><div><br><span id="yiv69668406result_box" class="yiv69668406" lang="en"><span class="yiv69668406hps"></span></span></div><div><span id="yiv69668406result_box" class="yiv69668406" lang="en"><span class="yiv69668406hps">pdb2gmx -f ion.pdb -posrefc 0</span></span></div><div><br><span id="yiv69668406result_box" class="yiv69668406" lang="en"><span class="yiv69668406hps"></span></span></div><div><span id="yiv69668406result_box" class="yiv69668406" lang="en"><span class="yiv69668406hps">Force Field :
 AMBER99SB-ILDN&nbsp; - Water TIP3P<br></span></span></div><div><br><span id="yiv69668406result_box" class="yiv69668406" lang="en"><span class="yiv69668406hps"></span></span></div><div><span id="yiv69668406result_box" class="yiv69668406" lang="en"><span class="yiv69668406hps">editconf -f conf.gro -bt cubic -box 3 3 3</span></span></div><div><br><span id="yiv69668406result_box" class="yiv69668406" lang="en"><span class="yiv69668406hps"></span></span></div><div><span id="yiv69668406result_box" class="yiv69668406" lang="en"><span class="yiv69668406hps">genbox -cp out.gro -cs spc216.gro -o 5.gro -p topol.top</span></span></div><div><br><span id="yiv69668406result_box" class="yiv69668406" lang="en"><span class="yiv69668406hps"></span></span></div><div><span id="yiv69668406result_box" class="yiv69668406" lang="en"><span class="yiv69668406hps">grompp -f minim.mdp -c 5.gro -p topol.top</span></span></div><div><br><span id="yiv69668406result_box"
 class="yiv69668406" lang="en"><span class="yiv69668406hps"></span></span></div><div><span id="yiv69668406result_box" class="yiv69668406" lang="en"><span class="yiv69668406hps">mdrun -s topol.tpr</span></span></div><div><br><span id="yiv69668406result_box" class="yiv69668406" lang="en"><span class="yiv69668406hps"></span></span></div><div><span id="yiv69668406result_box" class="yiv69668406" lang="en"><span class="yiv69668406hps">grompp -f nvt.mdp -c confout.gro -p topol.top -o md.tpr</span></span></div><div><br><span id="yiv69668406result_box" class="yiv69668406" lang="en"><span class="yiv69668406hps"></span></span></div><div><span id="yiv69668406result_box" class="yiv69668406" lang="en"><span class="yiv69668406hps">mdrun -s md.tpr</span></span></div><div><br><span id="yiv69668406result_box" class="yiv69668406" lang="en"><span class="yiv69668406hps"></span></span></div><div><span id="yiv69668406result_box" class="yiv69668406short_text" lang="en"><span
 class="yiv69668406hps">Whether</span> <span class="yiv69668406hps">the</span> <span class="yiv69668406hps">simulation</span> <span class="yiv69668406hps">is</span></span><span id="yiv69668406result_box" class="yiv69668406short_text" lang="en"><span class="yiv69668406hps"></span></span><span id="yiv69668406result_box" class="yiv69668406short_text" lang="en"> correct ?<span class="yiv69668406hps"></span></span><br><br><br></div><div><br></div><div><br></div><div></div></div></div><br><br></div></div></div></div><br><br></div></div></div></body></html>